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Anatoly B. Kolomeisky

Professor of Chemistry and Professor of Chemical and Biomolecular Engineering

Theoretical investigation of complex chemical and biophysical processes using the methods of statistical mechanics. Specific projects: 1) motor proteins; 2) cytoskeleton filaments; 3) polymer translocation through nanopores; 4) facilitated diffusion; 5) transport through membrane pores; 6) multi-partical non-equilibrium dynamics; 6) protein nucleation and crystallizations; 7) viscosity in biological systems, 8) protein-DNA interactions, 9) modeling of dynamics of nanocars.


A Simple Kinetic Model for Singlet Fission: A Role of Electronic and Entropic Contributions to Macroscopic Rates, A.B. Kolomeisky, X. Feng and A.I. Krylov, J. Phys. Chem. C 118, 5188-5195 (2014). 

A New Theoretical Approach to Analyze Complex Processes in Cytoskeleton Proteins, X. Li and A.B. Kolomeisky, J. Phys. Chem. B 118, 2966-2972 (2014).

Bulk Induced Phase Transitions in Driven Diffusive Systems, Y.-Q. Wang, R. Jiang, A.B. Kolomeisky and M.-B. Hu, Sci. Rep. 4, 5459 (2014).  

Collective Dynamics of Cytoskeletal Processive Motor Proteins, (R.T. McLaughlin, M.R. Diehl and A.B. Kolomeisky), Soft Matter, (2015).

Correlations and Symmetry of Interactions Influence Collective Dynamics of Molecular Motors,
(D. Celis-Garza, H. Teimouri and A.B.K.), J. Stat. Mech. P04013 (2015).

Development of Morphogen Gradient: The Role of Dimension and Discreteness, H. Teimouri and A.B. Kolomeisky, J. Chem. Phys. 140, 085102 (2014).

Development of Morphogen Gradients with Spatially Varying Degradation Rates, (B. Bozorgui, H. Teimouri and A.B.K.), submitted to J. Phys. Chem. B (2015).

 Dissecting the Effect of Morphology on the Rates of Singlet Fission: Insights from Theory, X. Feng, A.B. Kolomeisky and A.I. Krylov, J. Phys. Chem. C, 118, 19607-19617 (2014).

M.N. Artyomov, A.Y. Morozov and A.B.Kolomeisky, "Dynamics of Molecular Motors in Reversible Burnt-Bridge Models,"  Condens. Matter Phys. 13, 23801 (2010).

Dynamics of the Protein Search for Targets on DNA in the Presence of Traps, (M. Lange, M. Kochugaeva and A.B. K.), J. Phys. Chem. B 119, 12410-12416 (2015).

R.K. Das and A.B. Kolomeisky, "Facilitated Search of Proteins on DNA: Correlations are Important," Phys. Chem.-Chem. Phys. 12, 2999-3004 (2010).

J. Lin, A.B.Kolomeisky and A. Meller, "Helix-Coil Kinetics of Individual Polyadenylic Acid Molecules in a Protein Channel,"   Phys. Rev. Lett. 104, 158101 (2010).

Hydrolysis of Guanosine Triphosphate (GTP) by the Ras·GAP Protein Complex: Reaction Mechanisms and Kinetic Scheme, (M.G. Khrenova, B.L. Grigorenko, A.B.K., and A.V. Nemukhin), J. Phys. Chem. B 119, 12838-12845 (2015).

A.B. Kolomeisky “Motor Proteins and Molecular Motors.” CRC, Taylor and Francis, 2015.

Pathway Structure Determination of Complex Stochastic Networks with Non-Exponential Dwell Times, X. Li, A.B. Kolomeisky and A. Valleriani, J. Chem. Phys. 140, 184102 (2014).

Positive and Negative Impacts of Nonspecific Sites During Target Location by a Sequence-Specific DNA-binding Protein: Origin of the Optimal Search at Physiological Ionic Strength, A. Esadze, A.B. Kolomeisky and J. Iwahara, Nucl. Acids Res. 42, 7039-7046 (2014).

Protein Search for Multiple Targets on DNA, (M. Lange, M. Kochugaeva and A.B. K.),
J. Chem. Phys. 143, 105102 (2015).

Protein-Assisted DNA Looping: A Delicate Balance among Interactions, Mechanics, and Entropy,
(A.B.K.), Biophys. J. 109, 459-460 (2015).

Sequence Heterogeneity Accelerates Protein Search for Targets on DNA, (A.A. Shvets and A.B.K.), submitted to J. Chem. Phys. (2015).

Staying Together: Protein Molecules in Mesoscopic Clusters, (A.B.K.), Biophys. J. 109, 1759-1760 (2015).

Stochastic Kinetics on Networks: When Slow is Fast, X. Li, A.B. Kolomeisky and A. Valleriani, J. Phys. Chem. B, 118, 10419-10425 (2014).

The Role of Multifilament Structures and Lateral Interactions in Dynamics of Cytoskeleton Proteins and Assemblies, (X. Li and A.B.K.), J. Phys. Chem. B 119, 4653 (2015).

The Role of Source Delocalization in the Development of Morphogen Gradients, (H. Teimouri and A.B.K.), Phys. Biol. 12, 026006 (2015).

The Role of Static and Dynamic Obstacles in the Protein Search for Targets on DNA
(A.A. Shvets, M. Kochugaeva and A.B.K.), to appear in J. Phys. Chem. B (2015).

Theoretical Analysis of Degradation Mechanisms in the Formation of Morphogen Gradients,
(B. Bozorgui, H. Teimouri and A.B.K.), J. Chem. Phys. 143, 025102 (2015).

Theoretical Analysis of Dynamic Processes for Interacting Molecular Motors, (H. Teimouri, A.B.K. and K. Mehrabiani), J. Phys. A 48, 065001 (2015).

Theoretical Analysis of Selectivity Mechanisms in Molecular Transport Through Channels and Nanopores, (S. Agah, M. Pasquali and A.B.K.), J. Chem. Phys. 142, 044705 (2015).

Unimolecular Submersible Nanomachines. Synthesis, Actuation, and Monitoring (V. Garcia-Lopez, P.-T. Chiang, F. Chen, G. Ruan, A.A. Marti, A.B.K., G. Wang and J.M. Tour), to appear in Nano Lett. (2015).

Unveling the Hidden Structure of Complex Stochastic Biochemical Networks, A. Valleriani, X. Li and A.B. Kolomeisky, J. Chem. Phys. 140, 064101 (2014). 

L.V.F. Gomes and A.B. Kolomeisky Dynamics of Relaxation to a Stationary State for Interacting Molecular Motors.  J. Phys. A: Math. Theor., 51 2018: 015601

B. Bozorgui, H. Teimouri and A.B. Kolomeisky Physical-Chemical Mechanisms of Pattern Formation during Gastrulation.  J. Chem. Phys., 148 2018: 123302

J. Shin and A.B. Kolomeisky Surface-Assisted Dynamic Search Processes.  J. Phys. Chem. B 2018

Y. Zhang and A.B. Kolomeisky Theoretical Investigation of Distributions of Run Lengths for Biological Molecular Motor.  J. Phys. Chem. B 2018

M. Margaliot, Y. Zarai and A.B. Kolomeisky A Deterministic Model for One-Dimensional Excluded Flow with Local Interactions.  PLOS ONE, e0182074 2017

K. Banerjee, A.B. Kolomeisky and O. A. Igoshin Accuracy of Substrate Selection by Enzymes is Controlled by Kinetic Discrimination.  J. Phys. Chem. Lett., 8 2017: 1552-1556

A.A. Kornyshev, R. Twidale and A.B. Kolomeisky Current-Generating ’Double Layer Shoe’ with a Porous Sole: Ion Transport Matters.  J. Phys. Chem C, 121 2017: 7584-7595

A.M. Berezhkovskii, A. Szabo, T. Rotbart, M. Urbakh and A.B. Kolomeisky Dependence of the Enzymatic Velocity on the Substrate Dissociation Rate.  J. Phys. Chem. B, 121 2017: 3437-3442

K. Banerjee, A.B. Kolomeisky and O. A. Igoshin Elucidating Interplay of Speed and Accuracy in Biological Error Correction.  Proc. Natl. Acad. Sci. USA, 114 2017: 5183-5188

A.B. Kolomeisky How Viruses Enter Cells: A Story behind Bacteriophage T4.  Biophys. J., 113 2017: 3-4

A.A. Shvets and A.B. Kolomeisky Mechanism of Genome Interrogation: How CRISPR RNA-guided Cas9 Proteins Locate Specific Targets on DNA.  Biophys. J., 113 2017: 1416-1424

V. Garcia-Lopez, F. Chen, L.G. Nilewski, G. Duret, A. Alian, A.B. Kolomeisky, J.T. Robinson, G. Wang, R. Pal and J.M. Tour Molecular Machines Open Cell Membranes.  Nature, 548 2017: 567-572

Q. Wang, M.R. Diehl, B. Jana, M.S. Cheung, A.B. Kolomeisky and J. Onuchic Molecular Origin of the Weak Susceptibility of Kinesin Velocity to Loads and Its Relation to the Collective Behavior of Kinesins.  Proc. Natl. Acad. Sci. USA, 114 2017: E8611-8617

M.P. Kochugaeva, A.A. Shvets and A.B. Kolomeisky On the Mechanism of Homology Search by RecA Protein Filaments.  Biophys. J., 112 2017: 859-867

M.P. Kochugaeva, A.A. Berezhkovskii and A. Kolomeisky Optimal Length of Conformational Transition Region in Protein Search for Targets on DNA.  J. Phys. Chem. Lett., 8 2017: 4049-4054

T. Midha, A.K. Gupta and A.B. Kolomeisky The Effect of Side Motion in the Dynamics of Interacting Molecular Motors.  J. Stat. Mech., P073201 2017

H. Teimouri and A. B. Kolomeisky All-Time Dynamics in Complex Continuous-Time Random Walk Models.  J. Chem. Phys., 138 2013: 084110

K. Uppulury, A. K. Efremov, J. W. Driver, D. K. Jamison, M. R. Diehl and A. B. Kolomeisky Analysis of Cooperative Behavior in Multiple Kinesins Motor Protein Transport by Varying Structural and Chemical Properties .  Cell. Mol. Bioeng., 6 2013: 38-47

X. Banquy, G. W. Greene, B. Zappone, A. B. Kolomisky and J. N. Israelachvili Dynamics of Force Generation by Confined Actin Filaments.  Soft Matter, 9 2013: 2389-2392

B. Farrell, F. Qian, A. B. Kolomeisky, B. Anwari and W. E. Brownell Measuring Forces at the Leading Edge: A Force Assay for Cell Motility.  Integr. Biol., 5 2013: 204-214

X. Li and A. B. Kolomeisky Mechanisms and Topology Determination of Complex Chemical and Biological Network Systems from First-Passage Theoretical Approach.  J. Chem. Phys., 139 2013: 144106

A. B. Kolomeisky Mechanisms of Protein Binding to DNA: Statistical Interactions are Important.  Biophys. J., 104 2013: 966-967

A. B. Kolomeisky Motor Proteins and Molecular Motors: How to Operate Machines at the Nanoscale.  J. Phys.: Condens. Matter, 25 2013: 463101

R. Jiang, Y.-Q. Wang, A. B. Kolomeisky, W. Huang, M.-B. Hu and Q.-S. Wu Phase Diagram Structures in a Periodic One-Dimensional Exclusion Process.  Phys. Rev. E, 87 2013: 012107

A. B. Kolomeisky Physics of Protein Motility and Motor Proteins. .  J. Phys.: Condens. Matter, 25 2013: 370301

A. Veksler and A. B. Kolomeisky Speed-Selectivity Paradox in the Protein Search for Targets on DNA: Is It Real or Not?.  J. Phys. Chem. B, 117 2013: 12695-12701

P.-L. E. Chu, L.-Y. Wang, S. Khatua, A. B. Kolomeisky, S. Link and J. M. Tour Synthesis and Single-Molecule Imaging of Highly Mobile Adamantane-Wheeled Nanocars.  ACS Nano, 7 2013: 35-41

X. Li and A. B. Kolomeisky Theoretical Analysis of Microtubules Dynamics Using a Physical-Chemical Description of Hydrolysis.  J. Phys. Chem. B, 117 2013: 9217-9223

D. Panja, G. T. Barkema and A. B. Kolomeisky Through the Eye of the Needle: Recent Advances in Understanding Biopolymer Translocation.  J. Phys.: Condens. Matter, 25 2013: 413101

A. V. Akimov, C. Williams and A. B. Kolomeisky Charge Transfer and Chemisorption of Fullerene Molecules on Metal Surfaces: Application to Dynamics of Nanocars.  J. Phys. Chem. C, 116 2012: 13816-13826

K. Uppulury, A. K. Efremov, J. W. Driver, D. K. Jamison, M. R. Diehl and A. B. Kolomeisky How the Interplay between Mechanical and Nonmechanical Interactions Affects Multiple Kinesin Dynamics.  J. Phys. Chem. B, 116 2012: 8846-8855

A. B. Kolomeisky and A. Veksler How to Accelerate Protein Search on DNA: Location and Dissociation.  J. Chem. Phys., 136 2012: 12501

A. B. Kolomeisky and D. Lacoste Random Hydrolysis Controls the Dynamic Instability of Microtubules.  Biophys. J., 102 2012: 1274-1283

A. V. Akimov and A. B. Kolomeisky Unidirectional Rolling of Nanocars Induced by Electric Field.  J. Phys. Chem. C, 116 2012: 22595-22601

J. H. P. Schulz, A. B. Kolomeisky and E. Frey Current Reversal ad Exclusion Processes with History-Dependent Random Walks.  Europhys. Lett., 95 2011: 30004

A. V. Akimov and A. B. Kolomeisky Dynamics of Single-Molecule Rotations on Surfaces that Depend on Symmetry, Interactions and Molecular Sizes.  J. Phys. Chem. C, 115 2011: 125-131

A. B. Kolomeisky Formation of a Morphogen Gradient: Acceleration by Degradation.  J. Phys. Chem. Lett., 2 2011: 1502-1505

A. B. Kolomeisky and K. Uppulury How Interactions Control Molecular Transport in Channels.  J. Stat. Phys., 142 2011: 1268-1276

A. B. Kolomeisky Michaelis-Menten Relation for Complex Enzymatic Networks.  J. Chem. Phys., 134 2011: 155101

A. V. Akimov and A. B. Kolomeisky Molecular Dynamics Study of Crystalline Molecular Gyroscopes.  J. Phys. Chem. C, 115 2011: 13584-13591

I. V. Kupchenko, A. A. Moskovsky, A. V. Nemukhin and A.B.Kolomeisky On the Mechanism of Carborane Diffusion on a Hydrated Silica Surface.  J. Phys. Chem. C, 115 2011: 108-111

A. B. Kolomeisky Physics of Protein-DNA Interactions: Mechanisms of Facilitated Diffusion.  Phys. Chem. Chem. Phys., 13 2011: 2088-2095

J. W. Driver, D. K. Jamison, K. Uppulury, A. R. Rogers, A. B. Kolomeisky and M. R. Diehl Productive Cooperation among Processive Motors Depends Inversely on Their Mechanochemical Efficiency.  Biophys. J., 101 2011: 386-395

A. V. Akimov and A. B. Kolomeisky Recursive Taylor Series Expansion Method for Rigid-Body Molecular Dynamics.  J. Theor. Chem. Comp., 7 2011: 3062-3071

R. Wang, A. B. Kolomeisky, and M. Liu Spontaneous Symmetry Breaking on a Multiple-Channel Hollow Cylinder.  Phys. Rev. A, 375 2011: 318-323

J. W. Driver, A. R. Rogers, D. K. Jamison, R. K. Das, A. B. Kolomeisky and M. R. Diehl Coupling between Motor Proteins Determines Dynamic Behaviors of Motor Protein Assemblies.  Phys. Chem. Chem. Phys., 12 2010: 10398-10405

S. S. Konyukhov, I. V. Kupchenko, A. A. Moskovsky, A. V. Nemukhin, A. V. Akimov and A. B. Kolomeisky Rigid-Body Molecular Dynamics of the Fullerene-Based Nanocars on the Metallic Surfaces.  J. Chem. Theory Comput., 6 2010: 2581-2590

A. B. Kolomeisky Continuous-Time Random Walks at All Times.  J. Chem. Phys., 131 2009: 23414

R. K. Das and A. B. Kolomeisky Dynamic Properties of Molecular Motors in the Divided-Pathway Model.  Phys. Chem. Chem. Phys., 11 2009: 4815-4820

C. H. Sykes, A. Akimov and A. B. Kolomeisky Dynamics of Thioethers Molecular Rotors: Effect of Surface Interactions and Chain Flexibility .  J. Phys. Chem. C, 113 2009: 10913-10920

S.Khatua, J.M. Guerrero, K. Claytor, G. Vives, A.B. Kolomeisky, J.M. Tour and S. Link Micrometer-Scale Translation and Monitoring of Individual Nanocars on Glass .  ACS Nano, 3 2009: 351-356

D. Panja, G. T. Barkema and A. B. Kolomeisky Non-Equilibrium Dynamics of Single Polymer Adsorption to Solid Surfaces.  J. Phys. Condens. Matter, 21 2009: 242101

A. Mohan, A. B. Kolomeisky, M. Pasquali Effect of Charge Distribution on the Translocation of an Imhomogeneously Charged Polymer Through a Nanopore.  J. Chem. Phys., 128 2008: 125104-1:125104-7

A. B. Kolomeisky, S. Kotsev Effect of Interactions on Molecular Fluxes and Fluctuations in the Transport across Membrane Channels.  J. Chem. Phys., 128 2008: 085101-1:185101-6

A. B. Kolomeisky How Proteins Translate Through Pores: Memory is Important.  Biophys. J., 94 2008: 5547-1548

K. Tsekouras and A. B. Kolomeisky Inhomogeneous Coupling in Two-Channel Asymmetric Exclusion Processes.  J. Phys. A: Math Theor., 41 2008: 095002

R. K. Das, A. B. Kolomeisky Interaction between Motor Domains Can Explain the Complex Dynamics of Heterodimeric Kinesins.  Phys. Rev. E, 77 2008: 061912

A. Akimov, A. V. Nemukhin, A. Moskovsky, A. B. Kolomeisky, J. M. Tour Molecular Dynamics of Surface-Moving Thermally Driven Nanocars.  J. Chem. Theor. Comp., 4 2008: 652-656

M. N. Artyomov, A. Y. Morozov, A. B. Kolomeisky Molecular Motors Interacting with Their Own Tracks.  Phys. Rev. E, 77 2008: 040901(R)

A. G. Cherstvy, A. B. Kolomeisky, A. A. Kornyshev Protein-DNA Interactions: Reaching and Recognizing the Targets.  J. Phys. Chem. B, 112 2008: 4741-4750

R. K. Das, A. B. Kolomeisky Spatial Fluctuations Affect the Dynamics of Motor Proteins.  J. Phys. Chem. B, 112 2008: 11112-11121

Kolomeisky Research Group
Anatoly Kolomeisky

  • M.S. Chemistry (1991) Moscow State University
  • M.S. Chemistry (1996) Cornell University
  • Ph.D. Chemistry (1998) Cornell University
  • Center for Theoretical Biological Physics
  • Department of Chemical and Biomolecular Engineering
  • Institute of Biosciences and Bioengineering
  • Smalley-Curl Institute
  • Theoretical Physical Chemistry. Theoretical Biophysics. Statistical Mechanics of Complex Systems. Biological Transport. Thermodynamics of Electrolytes. Random Walks. Theory of Hydrophobicity.
Email: tolya@rice.edu
Phone: (713) 348-5672
Office: Anderson Biological Lab, 306